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Three-dimensional structure of bacteriophage T4 baseplate.

by single particle reconstruction, at 12 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w, Surface level: 2, Made by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1pdf, Made by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1pdi, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-1pdj, Made by Jmol

#7: Simplified surface model with fitted atomic model: PDB-1pdl, Made by Jmol

#8: Simplified surface model with fitted atomic model: PDB-1pdm, Made by Jmol

#9: Simplified surface model with fitted atomic model: PDB-1pdp, Made by Jmol

#10: Simplified surface model with fitted atomic model: PDB-2fl8, Made by Jmol

#11: Simplified surface model with fitted atomic model: PDB-3h3w, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1048
TitleThree-dimensional structure of bacteriophage T4 baseplate.
Mapmap contains the baseplate and the proximal part of the tail tube
SampleBacteriophage T4 baseplate-tail tube assembly
AuthorsKostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, vanRaaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG
DateDeposition: 2003-05-19, Header release: 2003-05-19, Map release: 2003-09-19, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1pdf, PDB-1pdi, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w, Surface level: 2, Made by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1pdf, Made by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1pdi, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-1pdj, Made by Jmol

#7: Simplified surface model with fitted atomic model: PDB-1pdl, Made by Jmol

#8: Simplified surface model with fitted atomic model: PDB-1pdm, Made by Jmol

#9: Simplified surface model with fitted atomic model: PDB-1pdp, Made by Jmol

#10: Simplified surface model with fitted atomic model: PDB-2fl8, Made by Jmol

#11: Simplified surface model with fitted atomic model: PDB-3h3w, Made by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-1pdf

CiteFit

PDB-1pdi

CiteFit

PDB-1pdj

CiteFit

PDB-1pdl

CiteFit

PDB-1pdm

CiteFit

PDB-1pdp

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNat. Struct. Biol., Vol. 10, Issue 9, Page 688-93, Year 2003
TitleThree-dimensional structure of bacteriophage T4 baseplate.
AuthorsVictor A Kostyuchenko, Petr G Leiman, Paul R Chipman, Shuji Kanamaru, Mark J van Raaij, Fumio Arisaka, Vadim V Mesyanzhinov, Michael G Rossmann
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia.
KeywordsBacteriophage T4 (chemistry), Cryoelectron Microscopy, Image Processing, Computer-Assisted, Microscopy, Electron, Models, Molecular, Protein Structure, Tertiary
LinksPubMed: 12923574, DOI: 10.1038/nsb970
Map
Fileemd_1048.map.gz ( map file in CCP4 format, 29414 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
2.9787193877551 A/pix
= 583.829 A
196 pix
2.9787193877551 A/pix
= 583.829 A
196 pix
2.9787193877551 A/pix
= 583.829 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.45 (by author), 2 (movie #1):
Minimum - Maximum: -7.64827013 - 10.34481144
Average (Standard dev.): 0E-8 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions196196196
Origin-98-98-97
Limit979798
Spacing196196196
Unit CellA= B= C: 583.8291 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.97872 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.97871938775512.97871938775512.9787193877551
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z583.829583.829583.829
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-98-98-97
NC/NR/NS196196196
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-7.64810.3450.000
Annotation Detailsmap contains the baseplate and the proximal part of the tail tube
Supplement
Images
Images
Sample
NameBacteriophage T4 baseplate-tail tube assembly
Number of Components1
Oligomeric Statethe complex has sixfold symmetry
Component #1: protein - baseplate-tail tube complex
Scientific namebaseplate-tail tube complex
Scientific Name of SpeciesEnterobacteria phage T4
Common Name of Speciesbacteriophage T4
NCBI taxonomy10665
StrainT4 18-,23-
Recombinant expressionYes
Natural SourceOrganelle: baseplate and tail tube
Engineered SourceExpression system: Escherichia coli BE
Experiment
Sample Preparation
Specimen Conc5 mg/ml
Specimen Support Detailsholey carbon
Specimen Stateparticle
BufferDetails: water
pH: 7
Vitrification
Cryogen NameETHANE
MethodBlot for 2 seconds before plunging
Imaging
MicroscopeFEI/PHILIPS CM300FEG/T
Date2001-01-30
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose25 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 45000, Calibrated: 47000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1200 nm - 5000 nm
Specimen Holder
Holder626 Single Tilt Cryotransfer System
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images15
Sampling Size14
Quant Bit Number8
ScannerZEISS SCAI
Detailsimages were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmmodel based projection matching
SoftwareSPIDER
CTF Correctioneach particle
Detailsmodified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly
Resolution By Author12 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections945
Applied SymmetryC6 (6 fold cyclic)
Atomic Model Fitting
Model #0
DetailsProtocol: laplacian filtered real space
Refinement Protocolrigid body
Target Criteriacorrelation coefficient
Refinement SpaceREAL
SoftwareSitus 2.0, Colores
Model #1
SoftwareSitus 2.0, Colores
Target Criteriacorrelation coefficient
DetailsProtocol: laplacian filtered real space
Refinement Protocolrigid body
Refinement SpaceREAL
Model #2
Target Criteriacorrelation coefficient
Refinement SpaceREAL
SoftwareSitus 2.0, Colores
Refinement Protocolrigid body
DetailsProtocol: laplacian filtered real space
Model #3
Refinement Protocolrigid body
Refinement SpaceREAL
SoftwareSitus 2.0, Colores
DetailsProtocol: laplacian filtered real space
Target Criteriacorrelation coefficient
Model #4
DetailsProtocol: laplacian filtered real space
Target Criteriacorrelation coefficient
Refinement Protocolrigid body
Refinement SpaceREAL
SoftwareSitus 2.0, Colores
Model #5
SoftwareSitus 2.0, Colores
Refinement Protocolrigid body
DetailsProtocol: laplacian filtered real space
Target Criteriacorrelation coefficient
Refinement SpaceREAL
Model #6
Refinement SpaceREAL
Target Criteriacorrelation coefficient
SoftwareSitus 2.0, Colores
DetailsProtocol: laplacian filtered real space
Refinement Protocolrigid body
Model #7
Target Criteriacorrelation coefficient
Refinement SpaceREAL
Refinement Protocolrigid body
SoftwareSitus 2.0, Colores
DetailsProtocol: laplacian filtered real space
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1048.xml (10.3 KB)
Map dataemd_1048.map.gz (3.5 MB)
Images1048.gif (53.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1048
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.8 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 6.9 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.3 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.8 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.2 MB
movie #7
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.8 MB
movie #8
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
movie #9
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.5 MB
movie #10
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.6 MB
movie #11
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5 MB